Strain identifier

BacDive ID: 133282

Type strain: Yes

Species: Paracoccus contaminans

Strain Designation: WPAn02, RKI16-01929

Strain history: CIP <- 2016, P. Kämpfer, Giessen Univ., Giessen, Germany: strain WPAn02

NCBI tax ID(s): 1945662 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 25118

BacDive-ID: 133282

keywords: genome sequence, 16S sequence, Bacteria, aerobe, Gram-negative, coccus-shaped

description: Paracoccus contaminans WPAn02 is an aerobe, Gram-negative, coccus-shaped bacterium that was isolated from contaminated axenic water microcosm.

NCBI tax id

  • NCBI tax id: 1945662
  • Matching level: species

strain history

@refhistory
421762016, P. Kämpfer, Giessen Univ., Giessen, Germany: strain WPAn02
118738CIP <- 2016, P. Kämpfer, Giessen Univ., Giessen, Germany: strain WPAn02

doi: 10.13145/bacdive133282.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Rhodobacterales
  • family: Paracoccaceae
  • genus: Paracoccus
  • species: Paracoccus contaminans
  • full scientific name: Paracoccus contaminans Kämpfer et al. 2016

@ref: 25118

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhodobacterales

family: Rhodobacteraceae

genus: Paracoccus

species: Paracoccus contaminans

strain designation: WPAn02, RKI16-01929

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotility
25118negative1 µm1 µmcoccus-shapedno
118738positivecoccus-shapedyes

colony morphology

  • @ref: 25118
  • colony size: 2 mm
  • colony color: beige
  • incubation period: 2 days
  • medium used: NA (Nutrient Agar)

Culture and growth conditions

culture medium

@refnamegrowthcompositionlink
25118NA (Nutrient Agar)yes
25118brain–heart infusion agaryes
25118TSA (Trypticase soy agar)yes
25118Reasoner's 2A agar (R2A)yes
25118MacConkey agaryes
42176MEDIUM 566- Reasoner's 2A agar for Flavobacterium micromatiyesDistilled water make up to (1000.000 ml);R2A agar (18.200 g)
118738CIP Medium 566yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=566

culture temp

@refgrowthtypetemperaturerange
25118positivegrowth10.0-45.0
25118nogrowth4psychrophilic
25118nogrowth45thermophilic
42176positivegrowth25mesophilic

culture pH

  • @ref: 25118
  • ability: positive
  • type: growth
  • pH: 5.0-7.5

Physiology and metabolism

oxygen tolerance

  • @ref: 25118
  • oxygen tolerance: aerobe

spore formation

  • @ref: 25118
  • spore formation: no

halophily

@refsaltgrowthtested relationconcentration
25118NaClpositivegrowth0.0-1.0 %(w/v)
25118NaClnogrowth2 %(w/v)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
25118309162-oxoglutarate-carbon source
25118161933-hydroxybenzoate-carbon source
2511816865gamma-aminobutyric acid-carbon source
25118178794-hydroxybenzoate-carbon source
2511817128adipate-carbon source
2511815963ribitol-carbon source
2511818305arbutin-carbon source
2511835391aspartate-carbon source
2511878208azelaate-carbon source
2511816383cis-aconitate-carbon source
2511816947citrate-carbon source
2511817057cellobiose-carbon source
2511816899D-mannitol-carbon source
2511828053melibiose-carbon source
2511816551D-trehalose-carbon source
2511865327D-xylose-carbon source
25118370543-hydroxybutyrate-carbon source
2511824265gluconate-carbon source
2511817859glutaric acid-carbon source
2511817268myo-inositol-carbon source
2511817240itaconate-carbon source
2511815603L-leucine-carbon source
2511815729L-ornithine-carbon source
2511817295L-phenylalanine-carbon source
2511862345L-rhamnose-carbon source
2511816828L-tryptophan-carbon source
2511868428maltitol-carbon source
2511836986mesaconate-carbon source
2511828037N-acetylgalactosamine-carbon source
25118506227N-acetylglucosamine-carbon source
2511818401phenylacetate-carbon source
2511817272propionate-carbon source
2511817148putrescine-carbon source
2511817814salicin-carbon source
251189300suberic acid-carbon source
2511817992sucrose-carbon source
2511815708trans-aconitate-carbon source
2511830089acetate+carbon source
2511815824D-fructose+carbon source
2511812936D-galactose+carbon source
2511817634D-glucose+carbon source
2511817306maltose+carbon source
2511816024D-mannose+carbon source
2511816988D-ribose+carbon source
2511817924D-sorbitol+carbon source
2511829806fumarate+carbon source
2511816977L-alanine+carbon source
2511830849L-arabinose+carbon source
2511815971L-histidine+carbon source
2511817115L-serine+carbon source
2511824996lactate+carbon source
2511815361pyruvate+carbon source

enzymes

@refvalueactivityec
25118catalase+1.11.1.6
25118cytochrome oxidase+1.9.3.1

Isolation, sampling and environmental information

isolation

@refsample typeenrichment culturegeographic locationcountryorigin.countrycontinent
25118contaminated axenic water microcosmR2A agar (Reasoner's 2A agar)
118738Other, Contaminant of an axenic E. coli culture in 7% NaClWeningerodeGermanyDEUEurope

isolation source categories

Cat1Cat2
#Engineered#Contamination
#Environmental#Aquatic
#Host#Microbial

taxonmaps

  • @ref: 69479
  • File name: preview.99_5288.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_19;96_1674;97_3137;98_3939;99_5288&stattab=map
  • Last taxonomy: Paracoccus contaminans subclade
  • 16S sequence: KX427102
  • Sequence Identity:
  • Total samples: 755
  • soil counts: 31
  • aquatic counts: 127
  • animal counts: 590
  • plant counts: 7

Safety information

risk assessment

  • @ref: 118738
  • biosafety level: 1
  • biosafety level comment: Risk group (French classification)

Sequence information

16S sequences

  • @ref: 25118
  • description: Paracoccus contaminans strain WPAn02 16S ribosomal RNA gene, partial sequence
  • accession: KX427102
  • length: 1397
  • database: nuccore
  • NCBI tax ID: 1945662

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Paracoccus contaminans strain RKI 16-01929T=LMG 29738T=CCM 8701T=CIP 111112T1945662.5plasmidpatric1945662
66792Paracoccus contaminans strain RKI 16-01929T=LMG 29738T=CCM 8701T=CIP 111112T1945662.3completepatric1945662

GC content

  • @ref: 25118
  • GC-content: 66.1
  • method: thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno73.176yes
gram-positiveno97.544yes
anaerobicno99.075yes
aerobicyes92.167no
halophileno83.842yes
spore-formingno96.56no
glucose-utilyes84.383yes
flagellatedno93.949no
thermophileno74.787no
glucose-fermentno92.201no

External links

@ref: 25118

culture collection no.: RKI 16-01929, LMG 29738, CCM 8701, CIP 111112

straininfo link

  • @ref: 91401
  • straininfo: 412579

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny27599853Paracoccus contaminans sp. nov., isolated from a contaminated water microcosm.Kampfer P, Aurass P, Karste S, Flieger A, Glaeser SPInt J Syst Evol Microbiol10.1099/ijsem.0.0014782016Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nucleic Acid Hybridization, Paracoccus/*classification/genetics/isolation & purification, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Water MicrobiologyTranscriptome
Genetics28596405Genome Sequence of Paracoccus contaminans LMG 29738(T), Isolated from a Water Microcosm.Aurass P, Karste S, Trost E, Glaeser SP, Kampfer P, Flieger AGenome Announc10.1128/genomeA.00487-172017Phylogeny
Phylogeny31913112Paracoccus aeridis sp. nov., an indole-producing bacterium isolated from the rhizosphere of an orchid, Aerides maculosa.Rai A, N S, G S, A S, G D, Ch S, Ch V RInt J Syst Evol Microbiol10.1099/ijsem.0.0039622020Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Glycolipids/chemistry, India, Indoleacetic Acids/chemistry, Nucleic Acid Hybridization, Orchidaceae/*microbiology, Paracoccus/*classification/isolation & purification, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, *Rhizosphere, Sequence Analysis, DNA, Ubiquinone/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorstitledoi/urljournalpubmedcatalogue
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ10.1099/ijsem.0.004332
25118P. A. Kämpfer, P.,Karste, S.,Flieger, A.,Glaeser, S. P.Paracoccus contaminans sp. nov., isolated from a contaminated water microcosm10.1099/ijsem.0.001478IJSEM 66: 5101-5105 201627599853
42176Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/34937
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar SchomburgBRENDA, the ELIXIR core data resource in 2021: new developments and updates10.1093/nar/gkaa1025Nucleic Acids Res. 49: D498-D508 202033211880
69479João F Matias Rodrigues, Janko Tackmann,Gregor Rot, Thomas SB Schmidt, Lukas Malfertheiner, Mihai Danaila,Marija Dmitrijeva, Daniela Gaio, Nicolas Näpflin and Christian von Mering. University of Zurich.MicrobeAtlas 1.0 betahttps://microbeatlas.org/
91401Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.StrainInfo: A central database for resolving microbial strain identifiers10.60712/SI-ID412579.1
118738Curators of the CIPhttps://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20111112Collection of Institut Pasteur (CIP 111112)